The money laundering charge can be used to coerce the owner in to pleading guilty to whatever else they want to add to the list -- whether or not there is a case for it. Considering the age of the site, one would speculate that the owner may have said no to something the government politely asked for, and then ended up getting their insides turned out as a result.

The EFF certainly could have done a better job on this one. I'm not familiar with the site, but this seems to be a very different situation than Craigslist ran in to.